title: Functional combination strategy for prioritization of human miRNA target.
abstract: MicroRNAs (miRNAs) are a class of non-coding RNAs known to play important regulatory roles through targets, which can affect human cell proliferation, differentiation, and metabolism. Overlaps between different miRNA target prediction algorithms (MTPAs) are small, which limit the understanding of miRNA's biological functions. However, the overlaps increase on functional levels, such as Gene Ontology (GO), Protein-Protein Interaction Network (PPIN) and pathways. Here, we performed prioritization on existing predicted target sets for each miRNA by considering all the possible combinations of 7 functional levels. After analyzing the results of both single and multiple functional levels, we found that functional combination strategies including pathways and GO performed better in the prioritization of human miRNA target. The combination which performed best was "Pathway+GO BP+GO MF+GO CC+Target+PPIN". For the prioritized result of this combination, the valid target had top ranking, and our method performed better than the MTPAs after comparison adopting the validated ranking levels. Top genes in ranking lists generated by this strategy were either validated by experiments or share same functions with the corresponding miRNA/its validated genes in disease related biological processes.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Yunpeng
authors.initials: Y
authors.lastname: Zhang
authors.forename: Yingying
authors.initials: Y
authors.lastname: Wang
authors.forename: Chunlong
authors.initials: C
authors.lastname: Zhang
authors.forename: Qiuyu
authors.initials: Q
authors.lastname: Wang
authors.forename: Xinrui
authors.initials: X
authors.lastname: Shi
authors.forename: Chunquan
authors.initials: C
authors.lastname: Li
authors.forename: Ruijie
authors.initials: R
authors.lastname: Zhang
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors
keywords: BP; CC; Functional prioritization; GO; Gene Ontology; Gene Ontology—Biology Process; Gene Ontology—Cellular Component; Gene Ontology—Molecular Function; MF; MTPA; PPIN; Pathways; Protein–Protein Interaction Network; TF; TSG; miRNA target prediction algorithms; tissue specific genes; transcription factor